The Australian Electoral Commission (AEC) will conduct a recount of votes in the Victorian federal seat of McEwen.

When counting closed at the weekend Labor's Rob Mitchell was declared the winner by seven votes. That has since been cut to a six vote margin.

The seat was held by Liberal Fran Bailey who demanded the recount, claiming some ballot papers were missing and others not accepted.

The recount of more than 100,000 ballot papers will begin tomorrow.

Mr Mitchell is surprised by the decision.

"It goes against everything that they have been saying. It is their call, their decision, but I think that they have been bullied into it by the accusations levelled at them by the Liberal Party," he said.

However Ms Bailey is claiming some ballots had been missed.

"They have found another vote for me today apparently going through preferences and this has been a hallmark of the inconsistencies of the process of the past last two and a half weeks."